Clarkson said in a newspaper column that the data lost by staff at HM Revenue & Customs was useless, and published his own bank details in the article to prove his point.
However, he was forced to apologise publicly after £500 was quickly removed from his account.
Clarkson gave his account number and sort code and hinted at his address. This was enough for him to lose the money.
"I opened my bank statement this morning to find out that someone has set up a direct debit which automatically takes £500 from my account," he wrote in a Sunday Times article.
"The bank cannot find out who did this because of the Data Protection Act and they cannot stop it happening again. I was wrong and I have been punished for my mistake."
The money was transferred to a charity, Diabetes UK, which did not require a signature to set up a standing order. Clarkson has now apologised and admitted that data loss is a serious issue.
"Contrary to what I said at the time, we must go after the idiots who lost the discs and stick cocktail sticks in their eyes until they beg for mercy," he said.